title: Bioinformatics for qualitative and quantitative proteomics.
abstract: Mass spectrometry is today a key analytical technique to elucidate the amount and content of proteins expressed in a certain cellular context. The degree of automation in proteomics has yet to reach that of genomic techniques, but even current technologies make a manual inspection of the data infeasible. This article addresses the key algorithmic problems bioinformaticians face when handling modern proteomic samples and shows common solutions to them. We provide examples on how algorithms can be combined to build relatively complex analysis pipelines, point out certain pitfalls and aspects worth considering and give a list of current state-of-the-art tools.
authors.affiliation: AG Algorithmische Bioinformatik, Institut für Informatik, Freie Universität Berlin, Berlin, Germany. bielow@mi.fu-berlin.de
authors.forename: Chris
authors.initials: C
authors.lastname: Bielow
authors.forename: Clemens
authors.initials: C
authors.lastname: Gröpl
authors.forename: Oliver
authors.initials: O
authors.lastname: Kohlbacher
authors.forename: Knut
authors.initials: K
authors.lastname: Reinert
mesh_terms: D000465:Algorithms; D010455:Peptides / Q000032:analysis; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods*
chemical_list: D010455:Peptides; D011506:Proteins